On Tue, Jun 15, 2004, nlxc wrote:
>
> I am running MD for a complex of protein and ligand under constant pressure
> condition with ibelly=1 (only 20 A around liagnd can move). I use
> "solvatecap complex WATBOX216 { x y z} 20" to add 20 A water around the
> center of ligand. I have used the above setting to try several different
> protein-ligand systems. After about 400ps MD, the density of some systems
> are equilibrated at around 0.8, some are around 0.5, some are around 1.2. My
> question is why there is so much variation among different systems. Is it
> normal or something wrong with my setting? Any suggestions are highly
> appreciated. Thanks in advance.
>
I am confused here. You can only run constant pressure MD for a periodic
system, but the "solvatecap" option does not create a periodic box. What is
the value of ntb that you are using? What version of Amber? I think we need
to know more about how you prepared the system, and what sorts of input
parameters you are using.
....dac
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Received on Wed Jun 16 2004 - 00:53:00 PDT
